Metacat

    public String getDocType(LSID lsid) {

      // example

      // returns rev;doctype

      String _docType = null;

        InputStream docStream = null;

        // example metacat query

        //

        ResourceBundle rb = ResourceBundle.getBundle("metacat-lsid");

      }//if

      else

      {

        response.setContentType("text/html");

        Writer nonout = null;

        StringBuffer xml = createResultDocument(xmlquery, qspec, nonout, user,

     sudo cp <hostname>-apache.key /etc/ssl/private 

4. Apache needs to be configured to request a client certificate when the 

   rules that configure Apache for SSL and client certificate authentication. 

   directory, editing pertinent values to match your system and running 

   changed to match the specifics of your system and Metacat deployment.) 

   ::

5. Enable the ssl module: 

/etc/init.d/tomcat6 stop

## backup the old war file

then

fi  

## remove the knb application directory

then

  echo "Removing the old metacat application directorties"

fi 

## copy the new war file into the webapps directory

## expand the war file

CURR_DIR=`pwd`

echo cd to $CURR_DIR

cd $CURR_DIR

###############################################################################

# Create Metacat External File Space

a2enmod jk

## copy in knb site file

then 

  if [ "${KNB_SITE_DIFF}" != "" ]

  then

  fi

fi

echo "Copying knb site file to /etc/apache2/sites-available/"

## enable knb site

echo "Enabling knb site"

METACAT=../build/metacat.jar

METACAT_CLIENT=../build/metacat-client.jar

UTILITIES=../lib/utilities.jar

QUERY=../test/performance_measure_query

TIME=2

TOMCATUSER=tao

my $listname = "list_of_docids";

my $username = "uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org";

my $password = "xxx";

# Insert your test code below (better if it prints "ok 13"

# (correspondingly "not ok 13") depending on the success of chunk 13

# of the test code):

my $username = 'uid=jones,o=NCEAS,dc=ecoinformatics,dc=org';

my $password = 'your-pw-goes-here';

			// Check if this is a simple read request that doesn't use the

			// "action" syntax

			// These URLs are of the form:

			String pathInfo = request.getPathInfo();

			if (pathInfo != null) {

				String[] path = pathInfo.split("/");

  <div class="code">&lt;workspace&gt;/metacat/test/test.properties</div>

  This should only hold one property: metacat.contextDir.  This should point to 

  the context directory for the metacat server you are testing.  For example:

  The test classes will use this to determine where to look for the server

  metacat.properties file.</p>

  You will need to verify that all test.* properties are set correctly:

  <ul>

    <li>test.printdebug - true if you want debug output, false otherwise </li>

    <li>test.mcUser - the first metacat test user ("uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org" should be fine)</li>

    <li>test.mcPassword - the first metacat test password ("kepler" should be fine)</li>

    <li>test.mcAnotherUser - the second metacat test user.  This user must be a member of the knb-usr 

  <p>For each Skin:</p>

  <ul>

  <li>View main skin page by going to:

  for each skin, where <skin_name> is in:

    <div class="code">default, nceas, esa, knb, lter, ltss, obfs, nrs, sanparks, saeon</div>  

  Note that the kepler skin is installed on a different metacat instance and can be found at:

     <li>Use your search to find a document</li>

     <li>Choose the link to a document - you should see document details

     <li>In a separate browser, try the shortcut to the doc:

     You should see the same results as going to the doc via search.</li>

     </ul>

  </li>

3. Double-check that Metacat's temporary folder, application.tempDir, is 

   writable by the apache user, usually www-data or apache. 

   are executable: register-dataset.cgi and ldapweb.cgi.

  ::

5. Restart Apache.

disable the 'show site list' setting before you can submit the form without 

errors. You may also wish to remove (or modify) the list of NCEAS-specific 

projects that appear in the default registry. To remove these form fields, 

and select the Skins Specific Properties Configuration option. On the skins 

configuration page, uncheck the boxes beside any form elements that you do not 

wish to appear in the registry.

  <title>Search</title>

  </head>

  <body>

  Search for:

For more information about each EarthGrid service and its WSDL file, navigate 

to the "services" page on your Metacat server 

Note that the AdminService and Version service that appear on this page are 

not part of EarthGrid.

   Set the Metacat URL in the Morpho preferences to point to your Metacat.

Creating Your Own Client

------------------------

supported by an OAI-PMH compliant data provider (also referred to as a 

repository). These methods are:

The OAI-PMH compliant data provider must accept requests from both HTTP GET 

and HTTP POST request methods. Responses from the data provider must be 

Users of the Metacat OAI-PMH Data Provider should be aware of the following issues:

  a 'deleted' status, indicating that a record in the metadata format 

  specified by the metadataPrefix is no longer available. Since Metacat does 

  not provide a mechanism for retrieving a list of deleted documents, the use 

  of the 'deleted' status is not supported in this implementation of the 

  OAI-PMH Data Provider. This represents a possible future enhancement.

  has not been determined how set hierarchies should be structured in 

  Metacat, this implementation of the OAI-PMH repository does not support 

  set hierarchies. This represents a possible future enhancement.

  OAI-PMH allows two levels of granularity: day granularity and seconds 

  granularity. Since the Metacat database stores the value of its 

  ``xml_documents.date_updated`` field in day granularity, it is the level 

Users of the Metacat OAI-PMH Harvester should be aware of the following issues:

  check to see whether a 'deleted' status is flagged for a harvested document, 

  and if it is, the document is correspondingly deleted from the Metacat repository.

  granularity. Since the Metacat database stores the value of its 

  ``xml_documents.last_updated`` field in day granularity, it is also the 

  level that is supported by both the Metacat OAI-PMH Data Provider and the 

   ::

3. Edit the deployment descriptor (``web.xml``) file, also in the WEB-INF 

   directory. Uncomment the servlet-name and servlet-mapping entries for the 

   ::

+----------------------------------------+----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+

| AbstractCatalog.secondsToLive          | 3600                                                                       | The lifetime, in seconds, of the resumptionToken.                                                                                               |

+----------------------------------------+----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+

|                                        | YYYY-MM-DDThh:mm:ssZ                                                       |                                                                                                                                                 |

+----------------------------------------+----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+

| Identify.repositoryName                | Metacat OAI-PMH Data Provider                                              | A name for the repository.                                                                                                                      |

+----------------------------------------+----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+

| Identify.earliestDatestamp             | 2000-01-01T00:00:00Z                                                       | Earliest datestamp supported by this repository                                                                                                 |

+----------------------------------------+----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+

+----------------------------------------+----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+

| Identify.adminEmail                    | mailto:tech_support@someplace.org                                          | Email address of the repository administrator.                                                                                                  |

+----------------------------------------+----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+

         -dn uid=jdoe,o=myorg,dc=ecoinformatics,dc=org \

         -password some_password \

         -metadataPrefix oai_dc \

   On Linux/Unix: 

         -dn uid=jdoe,o=myorg,dc=ecoinformatics,dc=org \

         -password some_password \

         -metadataPrefix oai_dc \

Command line options and parameters are described in the following table:

+-----------------------------+----------------------------------------------------+-----------------------------------------------------------------------------------------------------+

| -setSpec                    | ``-setSpec someSet``                               | Harvest documents belonging to this set. (Optional)                                                 |

+-----------------------------+----------------------------------------------------+-----------------------------------------------------------------------------------------------------+

+-----------------------------+----------------------------------------------------+-----------------------------------------------------------------------------------------------------+

   ::

   then the Harvester Registration page would be accessed at: 

   ::

.. figure:: images/screenshots/image065.jpg

   :align: center

   ::

   On Linux/Unix (bash shell): 

   ::

   then the Harvester Registration page would be accessed at: 

   ::

2. Enter and submit your Metacat account information. On the subsequent screen, 

   click Unregister to remove your site and discontinue harvests. 

Enabling Web Searches: Sitemaps

===============================

crawling. Currently, the only way for a search engine to crawl and index 

Metacat so that individual metadata entries are available via Web searches 

is with a sitemap. Metacat automatically creates sitemaps for all public 

Verify that your sitemap files are available to the Web by browsing to::

  <your_web_context>/sitemaps/metacat<X>.xml 

Registering a Sitemap

---------------------

# Tomcat dev deployment directory

# build.tomcat.dir=/usr/local/tomcat

build.tomcat.dir=/Users/leinfelder/tools/apache-tomcat-6

# install ant target uses this to determine where to drop 

# the war file in an installation.  Test classes will use

# this value to find metacat.properties

# CVS access to retrieve latest EML, seek and utilities 

cvsroot=:ext:${env.USER}@cvs.ecoinformatics.org:/cvs

workflowscheduler.context=workflowscheduler

authority.context=authority

3. Log in to PostgreSQL and create the 'metacat' user

4. Download Metacat from the `Metacat Download Page`_ and extract the archive

5. ``sudo mkdir /var/metacat; sudo chown -R <tomcat_user> /var/metacat``

7. ``sudo /etc/init.d/tomcat6 restart``

8. Configure Metacat through the Web interface

================== ===========================================================

File               Description

================== ===========================================================

                   Linux systems. 

                   Linux systems.

jk.conf            Sample JkMount configuration file used by Apache on 

                   Ubuntu/Debian Linux systems. 

        ServerName dev.nceas.ucsb.edu 

        ErrorLog /var/log/httpd/error_log 

        CustomLog /var/log/httpd/access_log common 

          AllowOverride None 

          Options ExecCGI 

          Order allow,deny 

          Allow from all 

        </Directory> 

          AllowOverride None 

          Options ExecCGI 

          Order allow,deny 

          Allow from all 

        </Directory> 

        JkMount /metacat ajp13 

        JkMount /metacat/* ajp13 

      </VirtualHost> 

  3. Copy the "workers.properties" file provided by Metacat into your Apache configuration directory (<apache_install_dir>/conf/).  Depending on whether you are installing from binary distribution or source, the workers.properties file will be in one of two locations:

  sudo a2dismod jk

  sudo a2enmod jk

::

5. Disable the default Apache site configuration:

    sudo chown -R <tomcat_user> /var/metacat

  ::

4. Restart Tomcat. Log in as the user that runs your Tomcat server (often "tomcat") and type:  

  ::

  Warning: Do not backup the files to the ``<web_app_dir>`` directory.  Tomcat will

  try to run the backup copy as a service.

  ::

  Note: Typically, Tomcat will look for its application files (WAR files) in the

  ``<tomcat_home>/webapps`` directory. Your instance of Tomcat may be configured to

    http://yourserver.yourdomain.com/yourcontext/

You should substitute your context name for "yourcontext" in the URL above

something else). If everything is working correctly, you should be presented

with Metacat's Authorization Configuration screen. Note that if you do not have

Tomcat integrated with Apache you will probably have to type

  You will see the individual modules get built. You should see a "BUILD

  SUCCESSFUL" message at the end.

  directory.

To run your new Metacat servlet, open a Web browser and type::

  http://yourserver.yourdomain.com/yourcontext/ 

something else. The servlet may require a few seconds to start up, but once it

is running, you will be presented with the Authorization Configuration screen.

  ::

10. Exit PostgreSQL:

  ::

3.  Restart Tomcat: 

  ::

  Tomcat will try to run the backup copy as a service.

3.  Copy the new Metacat WAR file in to Tomcat applications directory: 

  ::

4.  Restart Tomcat: 

include only certain events: events from a particular IP address, user, event 

type, or that occurred after a specified start date or before an end date. 

events since the log was initiated::

  http://some.metacat.host/context/metacat?action=getlog 

	</target>

	<target name="install" depends="build-metacat"

		<copy file="${dist.dir}/${metacat.context}.war"

			todir="${app.deploy.dir}" />

		<delete dir="${app.deploy.dir}/${metacat.context}" />

		<copy file="${dist.dir}/geoserver.war"

					todir="${app.deploy.dir}" />

		<copy file="${dist.dir}/metacat-index.war"

					todir="${app.deploy.dir}" />

		<tstamp>

			<format property="NOW" pattern="MM/dd/yyyy hh:mm:ss aa" />

		</tstamp>

		</copy>

		<chmod file="${deb.pkg.dir}/DEBIAN/postinst" perm="755" />

			todir="${deb.pkg.dir}/usr/share/metacat-${metacat.version}" />

		<copy file="./metacat-bin-${metacat.version}.tar.gz"

			tofile="${deb.pkg.dir}/metacat_${metacat.version}.orig.tar.gz" />

   xmlns:prod="http://example.org/prod"

   xmlns:xs="http://www.w3.org/2001/XMLSchema"

   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

  <items>

    <prod:product>

      <number xsi:type="xs:short">557</number>

      </dataFormat>

      <distribution>

        <online>

        </online>

      </distribution>

    </physical>

# Initialize a metacat client connection and log in as test user

t1 = time()

debug("[test] -- Processing Login")

response = mc.login('test', 'test', 'NCEAS')

t2 = time()

class MetacatClient:

        self.metacatUrlPath = urlPath

        self.metacatServer = server

        self.sessionid = None

debug("       host: $host ")

debug("************************************************** ")

query_template_file = open('squery.xml.tmpl', 'r')

query_template = query_template_file.read()

# Initialize a metacat client connection and log in as test user

t1 = time()

debug("[test] -- Processing Login")

response = mc.login('test', 'test', 'NCEAS')

t2 = time()

  <identifier>jones.204.22</identifier>

  <title>This is a test data set with taxonomic coverage</title>

  <originator>

# Set this to the location of the metacat application context

# directory.  The tests will use this to find metacat.properties

            MetacatPopulator mp = new MetacatPopulator(

                    "http://knb.ecoinformatics.org/knb",  

                    /*"http://localhost:8080/knb"*/

                    /*"msucci"*//*"connolly.301"*/ 

                    "tao.1.1", //"frog", 

                    "uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org", 

	  /**Constants*/

	  private static String SRBDATAFILEDIR = "/home/tao/data-file/IPCC"; // Dir for storing srb data file

	  private static String DOCLISTFILE       = "docidList"; // File name which stores IPCC document id

	  private static String USERNAME          = "uid=dpennington,o=LTER,dc=ecoinformatics,dc=org";

	  private static String PASSWORD           = "password";

	  private static String TABLEONLINEURL= "/eml:eml/dataset/dataTable/physical/distribution/online/url";

  public void testGetBaseUrlFromSchemaURL()

  {

      String baseURL = XMLSchemaService.getBaseUrlFromSchemaURL(url);

      assertTrue("The base url should be "+base, baseURL.equals(base));

      url = "www.example.com/example.xsd";

      baseURL = XMLSchemaService.getBaseUrlFromSchemaURL(url);

      assertTrue("The base url should be "+null, baseURL==null);

      baseURL = XMLSchemaService.getBaseUrlFromSchemaURL(url);

      assertTrue("The base url should be "+url, baseURL.equals(url));

  }

    <context-param>

      <param-name>metacat.properties.path</param-name>

      <description>The metacat.properties file for sibling metacat deployment. Note that the context can change</description>

    </context-param>

> org.ietf.jgss.<span class="tooltip" title="included in standard JRE/JDK libraries">GSSCredential</span> credential = server.get(<span class="tooltip" title="MyProxy username">username</span>, <span class="tooltip" title="MyProxy passphrase">passphrase</span>, <span class="tooltip" title="Credential lifetime in seconds">lifetime</span>);

> 

> // 2. Connect to Metacat via GSI+HTTPS

> edu.ucsb.nceas.metacat.client.Metacat client 

>     = edu.ucsb.nceas.metacat.client.MetacatFactory.createMetacatConnection(metacatUrl);

> String loginResult = client.login(credential);

>       IDs, which will generally be LDAP DNs.  You can do this in a map

>       file that starts out in

>       <code>metacat/src/gsimap.properties</code> and gets deployed to

>       modify it in either place, but it will be overwritten each time

>       you redeploy Metacat if you change it in Tomcat's installation

>       directory.</p>

> 

>       <p>Short answer: replace "<code>https</code>" with

>       "<code>httpg</code>".</p>

>       <p>becomes</p>

> 

>       <p>Long answer: The URL in the example above,

>       uses the <code>HTTPS</code> protocol.  However, actually

>       handling that connection requires a protocol handler that

>       understands GSI+HTTPS instead of plain HTTPS.  Fortunately,

######## Workflow engine section              #########################################

executionEngine.endPointAddress=http://localhost:8080/axis2/services/KeplerWebService

######## junit test section  ################

test.printdebug=true

test.mcUser=uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org

test.mcPassword=kepler

test.mcAnotherUser=uid=test,o=NCEAS,dc=ecoinformatics,dc=org

       to be carried out once.

    -->     

  <xsl:variable name="ids" select="//*[@id!='']"/>

  <xsl:template match="/">

    <oai_dc:dc xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" 

       to be carried out once.

    -->     

  <xsl:variable name="ids" select="//*[@id!='']"/>

  <xsl:template match="/">

    <oai_dc:dc xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" 

       to be carried out once.

    -->     

  <xsl:variable name="ids" select="//*[@id!='']"/>

  <xsl:template match="/">

    <oai_dc:dc xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" 

			<head>

				<title>Search Results</title>

				<link rel="stylesheet" type="text/css"

				<script language="Javascript" type="text/JavaScript"

				<script language="Javascript" type="text/JavaScript"

				<script language="JavaScript">

					<![CDATA[

					function submitform(action,form_ref) {

					</xsl:attribute>

					<td class="text_plain">

							method="POST">

							<xsl:attribute name="name">

								<xsl:value-of select="translate(./docid, '()-.', '____')" />

				<tr class="searchresultsdivider">

					<td colspan="5">

						<img

							width="1" height="1" />

					</td>

				</tr>

		<!-- General, non-citation, metadata display-->

		<html xmlns="http://www.w3.org/1999/xhtml" xmlns:dri="http://di.tamu.edu/DRI/1.0/" xmlns:i18n="http://apache.org/cocoon/i18n/2.1">

		<xsl:call-template name="documenthead"/>

		<body id="Overview">

		<div id="main_wrapper">

								<img src="knb/style/skins/mets/cc-zero.png"/>

							</a>

							<a href="http://opendefinition.org/">

							</a>

						</div>

					</xsl:if>

						<i18n:text>xmlui.dri2xhtml.METS-1.0.license-cc0</i18n:text>

						<xsl:text> &#160; </xsl:text>

						<a href="http://creativecommons.org/publicdomain/zero/1.0/" target="_blank">

						</a>

						<a href="http://opendefinition.org/">

						</a>

					</div>

				</xsl:otherwise>

<html>

<head>

<title>Metacat Upload/Delete Interface</title>

</head>

<body class="emlbody">

datamanager.password=datamanager

datamanager.maxconnections=10

#datamanager.srb.endpoint=

#datamanager.srb.machinename=

Identify.earliestDatestamp=2000-01-01T00:00:00Z

Identify.deletedRecord=no

# Append something unique like .1, .2, etc to 'Identify.description' for each occurrence

# List the supported metadataPrefixes along with the class that performs the associated crosswalk

Crosswalks.oai_dc=edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml2oai_dc

Crosswalks.eml-2.0.0=edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml200

######## junit test section  ################

test.printdebug=true

test.workflowSchedulerUrl=http://localhost:8080/workflowscheduler/scheduler

test.mcUser=uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org

test.mcPassword=kepler

test.mcAnotherUser=uid=test,o=NCEAS,dc=ecoinformatics,dc=org

test.lterUser=uid=knbuser,o=LTER,dc=ecoinformatics,dc=org

test.lterPassword=b1gf1$h

test.testProperty=testing

######## Developers Section #########################################

    sys.exit(1)

print "Logging into destination server"

dest.login('username','password','NCEAS')

print "Open docid list and loop"

class MetacatClient:

        self.metacatUrlPath = urlPath

        self.metacatServer = server

        self.sessionid = None

    sys.exit(1)

print "Logging into destination server"

dest.login('user','password','NCEAS')

print "Logging into source server"

    echo "USAGE: $0 docidfile"

    exit 1

fi 

read metacatBaseURL

echo 'Please type KNB user name (It should look like "uid=tao,o=NCEAS,dc=ecoinformatics,dc=org")'

read username

#variables

JUNIT=/usr/local/devtools/apache-ant/lib/junit-4.3.1.jar

PROJECT=/home/tao/project/metacat

TOMCATUSER=tao

my $metacat1_url = "http://dataknp.sanparks.org/sanparks/metacat";

my $username = "uid=judithk,o=SANParks,dc=ecoinformatics,dc=org";

my $password = "xxxxxx";

#my $username = "uid=leinfelder,o=NCEAS,dc=ecoinformatics,dc=org";

#my $password = "xxxxxx";

      long before = System.currentTimeMillis();

      // Attributes != Paramters but there is no setParameter

      Enumeration e = request.getParameterNames();

      while( e.hasMoreElements() ) {

	 * In the web.xml of the Metacat-index context, there is a parameter:

	 * <context-param>

     * <param-name>metacat.properties.path</param-name>

     * <description>The metacat.properties file for sibling metacat deployment. Note that the context can change</description>

     *  </context-param>

     *  It points to the default metacat context - knb. If we rename the context, we need to change the value of there.

Index configuration

----------------------------

Metacat-index is deployed as a separate web application (metacat-index.war) and should be deployed 

is desired and can safely be omitted if it will not be utilized for any given Metacat deployment.

During the initial installation/upgrade, an empty index will be initialized in the configured "solr-home" location.

is used to configure GeoServer to use this shared data directory. To further 

configure GeoServer, use the Web-based configuration utility, 

which is available at: http://your.server.com/context/geoserver.jsp 

Common configuration tasks include:

To add a map to a Web page, simply include the map interface using an iframe:: 

  <iframe scrolling="no" frameborder="0" width="780" height="420" 

  </iframe>

the default map interface. If you plan to customize the map interface, copy

the map.jsp file into your skin's directory (either the default or 

customized skin directory). 

  cp -r style/common/spatial/map.jsp /style/skins/<myskin>/spatial

Configuring the Size and Initial Extent of the Map

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

:doc:`configuration` for directions). Once the file has been copied, you can 

modify the map's initial extent in: ``${skin.dir}/spatial/map.jsp``.

show the entire globe. The ``initMap()`` function should also be given the skin 

name so that spatial search results can be correctly styled.

::